biomed week 1 and 2 Flashcards
1
Q
covalent bonds can be … and … in nature
A
polar and non polar
2
Q
electronegativity is the …
A
affinity of an atom for electrons
3
Q
what are the three factors electronegativity is determined by
A
- protons in nucleus
-distance electrons are from the nucleus - shielding of electrons from the nucleus
4
Q
what does a difference in electronegativity of covalent bond forming atoms > 0.5 signify?
A
atom with higher electronegativity will attract more elctrons than the other
5
Q
what are the three van de waals forces?
A
dipole - dipole (strongest)
dipole induced dipole
induced dipole - induced dipole (weakest)
6
Q
what is an example of a dipole dipole interaction
A
H bonding
7
Q
how do hydrophobic non covalent bonds interact in the cell membrane
A
cluster on the surface of the membrane proteins
and
cluster in the interior of soluble proteins
8
Q
what are non covalent ionic interactions
A
attractions between oppositely charged molecules
when they occur between amino acid side chains of protiens, ionic bonds are reffered to as side bridges
9
Q
functional groups are what form of bonding
A
non covalent bonding patterns based on their polarities
10
Q
what is the reason that energy is released upon cleaving the phosphoryl group?
A
charges close together want to repeal, releasing energy
11
Q
what are two things monosaccharides usually include?
A
minimum of three C’s
hydroxyl groups plus either an aldehyde or a ketone group
(generic naming is based on the number of carbons)
12
Q
are monosaccarides linear or cyclic?
A
can be either
13
Q
what kind of bonds do monosaccharides make to form disaccharides or polysaccharides?
A
glycosidic bonds
14
Q
fatty acids attach to a gylcerol backbone to create a mono di or triglycerides using what kind of bond?
A
ester linkage
15
Q
amino acids use what kind of bonds to be incorperated into protiens?
A
peptide bonds
16
Q
what is the general structure of nucleotides
A
nitrogenous base ( purines - double ring structure, pyrimidines - single ring structure) , 5 carbon sugar and phosphate group(s)
17
Q
nucleotides form nucleic acids via a ….. bond
A
phosphodiester
- strongest covalent linkage
18
Q
specific examples of oxireductases include
A
dehydrogenase and oxidases
19
Q
what do dehydrogenases do?
A
remove Hs and donate them to a molecule other than oxygen
20
Q
what do oxidases do?
A
remove Hs and donate them to oxygen
21
Q
transferases
A
synthesize molecules by catalyzing the transfer group from one molecule to another
often use nucleophilic substitution
22
Q
what are two specific transferases
A
kinases
- transfer a phosphate group from ATP to another non water molecule
polymerases
- transfers a monomer to a polymer especially wrt DNA and RNA
X transferases
- transfers “X” from one molecule to the other
- changes the ending of name of the group
being transfered to “ yl
23
Q
what do hydrolases include
A
NUCLEOPHILIC SUBSTITUTION
catalyze hydrolysis reactions
phosphatases
- hydrolyse nonophosphate esters (AMP but not ATP) to release a phosphate group
ATPases
- hydrolyse ATP to release a phosphate group
- X ases where X refers to the molecule being
broken apart
- ex. peptidases hydrolyse peptides to
release smaller fragments
24
Q
what are the three types of reactions catalysed by lyases?
A
addition
- adds one molecule to another across a 2X or
3X carbon bond
- hydratase
elimination
- removed atoms in a molecule to create a double bond
- dehydratases , decarboxylases
condensation
- synthase
- joins two molecules creating a C-C bond
25
what is the name of the reaction where ATP donates a phosphate
kinase
26
what is unique about lyases
they break down molecules without water
26
what is unique about a synthase
a synthase is a type of lyase that can break covalent bonds without the use of ATP
26
what enzyme often breaks a bond and forms a double bond
lyases
27
hydrolase versus hydratase
versus hydrolysis
hydrolase catalyzes an addition of a water molecule across a double bond
- phosphatases
- hydrolyse monophosphate esters
hydratase enzymes catalyse addition of water molecules , double bond gets converted to single bond
hydrolases catalyze hydrolysis reactions
27
decarboxylases is an example of what enzyme? and carboxylases are an example of what enzyme?
lyases
ligases
27
what are isomerases?
they switch isomerize (rearrange groups within a molecule)
27
what are the three types of isomerases
mutases
- transfer functional groups intramolecularly
epimerases
- interconvert the groups around an asymmetric carbon in a molecule that has more than one asymetrical carbon
racemases
- interconvert the groups around an asymetrical carbon in a molecule that only has one asmetrical carbon
28
what is the function of ligases
ligases create bonds between two molecules
with the use of an ATP molecule
"X ligases" and "X " synthetases
- X refers to the name of the molecules being joined or the molecule being created
29
what is the first law of thermodynamics
energy in the universe is constant but energy forms will change
30
what is enthalpy?
the energy contents of the bonds within a system
we tend to measure this in change that occurs when reactants go to products
can be measured by heat change in a system
31
a reaction that releases heat is
exothermic negative H
tends to be spontanous
32
a reaction that absorbs heat is
endothermic positive H
tends to not be spontaneous but depends
33
what is the definition of entropy
how spread out or dispersed energy is in a system
34
increase in entropy means that the energy in the system is
more dispersed
35
what is the second law of thermodynamics
energy disperses or spreads out unless it is hindered from doing so
36
what does gibbs free energy
measures the energy difference between the products and reactants and takes into account both entropy and enthalpy
37
what is the gibbs free energy equation
triangleG = triangleH - TtriangleS
38
negative triangle G is
an exergonic reaction = spontaneous
39
positive triangle G is
an endergonic reaction = non spontaneous
40
gibbs free energy is dependant on
temperature, pH and relative concentrations of products and reactants
41
a negative triangleH will cause a more ...
spontaneous reaction
42
a positive triangleS will cause a more .....
spontaneous reaction
43
a positive triangleH and a negative triangleS will ...
never be spontaneous
44
non standard gibbs free energy is when
when both reactants and products are both not at 1M
45
gibbs free energy equation
triangleG =triangleG knot+ RT inverse log of products / reactants
46
how does gibbs free energy change when the reactants are increased compared to the products
triangleG becomes more negative, more likely to be exergonic
47
how does gibbs free energy change when the reactants are reduced compared to the products
more positive triangleG
48
even reactions with a positive triangleG can develop into exergonic reactions if the .... are substancially greater than the .....
reactants , products
49
gibbs free energy coupled reactions are
additive, sum of triangleG
50
the high energy phosphodiester bond , when broken, has a negative triangle G, that energy can be coupled with another reaction with a positive triangleG
the net reaction is ...... if triangleG of ATP is negative enough to counteract endergonic triangle G of the coupled reaction
exergonic
51
why are NADH and FADH2 indirect energy
because they need to be oxidized in the mitochondria and they need to go to the ETC to make ATP
52
gluconeogenesis purpose and location
makes glucose from precursor molecules
mitochondria and cytosol
53
glycogenesis purpose and location
makes glycogen to store glucose
cytosol
54
fatty acid synthesis purpose and location
makes fatty acids from Acetyl CoA
cytosol
55
lipogenesis purpose and location
adds fatty acids to a glycerol backbone to make triglyceride lipids
cytosol
56
ketogenesis purpose and location
makes ketone bodies from acetyl CoA
mitochondria
57
pentose phosphate shunt purpose and location
shunts glucose into the creation of various 5 Carbon sugars and NADPH
cytosol
58
glycogenolysis purpose and location
breakdown of glycogen to release glucose. glucose can then enter glycolysis to produce energy
cytosol
59
glycolysis purpose and location
breakdown of glucose to pyruvate to produce energy (NADH and ATP) After glycolysis pyruvate can be converted to acetyl coA to enter the CAC to produce more energy
60
beta oxidation purpose and location
breakdown of fatty acyls to acetyl CoA to produce energy ( NADH , FADH2) . Acetyl CoA can enter the CAC to produce more energy
mitochondria
61
ketolysis produce and location
breakdown of ketone bodies to acetyl CoA Acetyl CoA can enter the CAC to produce more energy
mitochondria
62
Citric Acid Cycle purpose and location
breakdown of citrate (made from Acetyl CoA and oxaloacetate) to produce energy (NADH, FADH2 , ATP)
mitochondria
63
glycolysis aerobic versus anaerobic
aerobic - pyruvate enters CAC and undergoes oxidative phosphoralization leading to the net production of 32 ATP molecules
anaerobic - pyruvate converts to lactate through anaerobic glycolysis
64
why does conversion of pyruvate to acetyl Coa only happen under aerobic conditions
ATP is needed to convert pyruvate to acetyl CoA. without oxygen, no ATP can be made in oxidative phosphorilization
65
with a lack of oxygen, pyruvate converts to lactate rather than .... why?
Acetyl CoA, because it regenerates NAD+
66
what are the substrates in gluconeogenesis
mitochondria:
certain amino acids (make pyruvate and oxaloacetate)
cytosol:
lactate
glycerol
67
why does the liver release glucose?
to raise blood sugar levels when they are low
68
what is the energy input for glycogenesis?
anabolic process
ATP
- not recuperated via glycolysis
UTP
- P breaking off UTP, similar to ATP breaking off P
69
what does the pentose phosphate shunt make?
NADPH (used for fatty acid synthesis)
5 C sugars (such as ribose - 5- P for nucleotide synthesis
70
what energy is produced in beta oxidation?
NADH , FADH2
71
in beta oxidation, what are the fats then broken down into? then what happens if we want more energy?
acetyl CoA, enters the CAC
72
excess glucose can divert to make ...
fatty acids
73
if you dont need fatty acids for energy, how do you store them for later retrieval and use ?
triglycerides
74
lipolysis releases fatty acids from ...
triglycerides
75
why are triglycerides useful for energy
compared to glycogen, TGs take up less space therefore they can store more energy
76
the liver can make ketone bodies from ... this is called ...
acetyl CoA , ketogenesis
77
ketone bodies are broken down to make ...
acetyl CoA
78
any cycle that can lead to the production of acetyl CoA can feed into ... to ....
CAC , make more energy
79
what three pathways feed into CAC
glycolysis, beta oxidation and amino acid metabolism
80
the ETC is found in the
inner mitochondrial membrane
81
The ETC takes electrons from ... and ... and passes then down the chain of electron carriers with ...
NADH and FADH2, increasing affinty
82
there are ... ways that a N can be incorporated into an amino acid .... (indirect) ... .. (indirect) and direct incorporation
transamination and transamidation
83
transamination involves .... an .... group from a amino acid to an ....
transferring , amino , alpha ketoacid
84
amino acid and alpha keto acid pairs
alanine and .....
glutamate and .....
aspartate and ....
pyruvate
alpha ketoglutarate
oxaloacetate
85
transaminations require coenzyme ...
pyridoxal phosphate PLP (vitamin B6 )
86
transamidation is similar to transamination, except
the N comes from amido instead of amino
87
direct amino acid anabolism is ...
the addition of N directly from ammonia
88
what three amino acids are in the glutamate family
glutamine(direct incorp) , proline and arginine( transamination)
89
what 5 amino acids are in the aspartate family
asparagine(direct incorp) , lysine , methonine , theronine and isoleucine
incorporation of N via transamination
90
what three amino acids are in the pyruvate family
alanine , valine and leucine
incorp of N via transamination
91
what two amino acids are in the serine family
cysteine and glycine
incorp by transamination
92
to be used as a coenzyme, folate first converts to ...
THF
93
folate enzymes assist in ...
1-C transfers (transfers of methyl groups)
ex.
ser to glycine
making purines and pyrimidines
94
what three amino acids are in the aromatic family
tryptophan , tyrosine and pheynlalanine
95
phenylketouria (PKU) is a recessive disorder with a deficiency in ..... which cases a build up of ... which is then converted to phenylketone and excreted in urine
phenylalanine hydroxlase
Phe
96
what amino acid is in the histidine family
histamine
97
PVT TIM HALL
what are the dietary essential amino acids?
pyr
Val
Tyr
T
Iso
Meth
Histine
Arg
Lysine
Leucine
98
what are the two deamination pathways?
general - glutamine synthase reaction (extra hepatic to liver)
muscle to liver - glucose alanine cycle
- results in alanine carrying N to the liver to make
urea
99
describe two ways for N to get from the extra hepatic tissues to the liver
amino acid transport
urea cycle
100
describe the glucose alanine cycle
working muscles break down amino acids to release alanine, alanine gets released in the blood stream during high amounts of energy demand, the liver takes it up and converts it to glucose through gluconeogenesis providing a source for other tissues
101
where does the urea cycle occur
liver
102
the urea cycle is a combination of:..... and .... to make ....
ornithine and carbamoyl phosphate to make citulline
103
through a series of reactions in the urea cycle the products are:
urea and ornithine (used to start the cycle over again)
104
how many Ns does urea have? from where?
2, carbamoyl phosphate and aspartate
105
where does carbamoyl phosphate come from?
C and O come from bicarbonate and the P comes from ATP, N comes from ammonia
106
arginase is only found in the ...
liver
107
what is the cost of ATP to make urea
4, 2 ATP for each amino group
108
urea connects to the CAC via
fumarate
109
in the urea cycle, Asp donates a N and leaves as ... which enters the CAC
fumerate
110
oxaloacetate can undergo transamination to make ..
Asp
111
once the amino acid group has been removed, the remaining C skeletons can be classified as: ......... and ......
Glucogenic
Ketogenic
112
glycolysis can be divided into two main phases :
preparative phase and ATP genrating phase
113
how many ATP are required in the prepatory phase of glycolysis?
2
114
how many ATP are created during the generating phase of glycolysis
4
NET 2 gained
115
how many NADH are generated per glucose molecule and where does it go?
2 and it goes to the ETC
116
what are the three irreversible reactions of glycolysis
glucose -> glucose 6 phosphate
fructose 6 phosphate -> fructose 1,6 biphosphate
phosphenolpyruvate -> pyruvate
117
gluconeogenesis occurs in the
liver and kidney
118
gluconeogeneisis is especially important in ...
fasting
119
is gluconeogenesis simply a reverse of glycolysis?
no, there are irreversible steps
120
lactate once in liver is converted back to
pyruvate
121
what is the cori cycle
the conversion of lactate to glucose through glycolysis (pyruvate first) and glyconeogenesis between the muscle and liver transported through the blood
122
glycerol can enter gluconeogensis pathway by converting to
DHAP
123
glucogenic amino acids can enter gluconeogensis by ...
being converted directly into pyruvate or into a citric acid cycle intermediate
124
alanline can be converted to .... in the ..
pyruvate, mitochondria
125
glucogenesis begins in the ...
mitochondria
126
lactate is converted into pyruvate in the ...
cytosol, it is then immediately shuttled into the mitochondria
127
once pyruvate is in the mitochondria it is then converted into ...
oxaloacetate
128
oxaloacetate can not cross into .. and therefore requires shuttle systems
the mitochondria
129
Malate shuttle is used when starting substrate is
alanine
oxaloacetate is converted to malate
130
lactate is converted to ... in the cytosol .... then enters into the mitochondria and is converted into ... , .... is then converted into phosphophenylpyruvate which is then shuttled into the mitochondria to continue with gluconeogenesis
pyruvate
pyruvate
oxaloacetate
oxaloacetate
131
an acid is a molecule that can give up a
H+
HCl
132
a base is a molecule that can give up an
OH-
NaOH, when added to water it completely ionized
133
weak acid CH3COOH will ..... when added to water
partially ionize
134
henderson hassleback equation is
pH = Pka + log (base / acid)
135
weak acid will buffer ... unit above or below the pKa
1
136
the henderson hassleback equation calculates
pH of a solution given the pKa of a weak acid or base and the concentration of the protonated or deprotonated forms
137
when salt and acid are equal what is the resulting pH
4.74
138
what buffer is used in the extracellular fluid
bicarbonate - carbonic acid buffer
139
what buffer is used in the RBC
Hb buffer system
140
what buffer is used intracellularly
phosphate buffer
141
protiens act as intracellular .......
plasma buffers
142
the bicarbonate - carbonic acid buffer is in equilibrium with dissolved CO2 because
carbonic anhydrase action
143
the bicarbonate carbonic buffer is the most effective
extracellular buffer
144
why is bicarbonate buffer so effective?
carbonic andrahase rapidly catalyzes the formation of carbonic acid from water and carbon dioxide
carbonic acid (protonated) dissociates into bicarbonate (deprotonated) and H+
145
what is important about carbon dioxide formation in the tissues
when Co2 is produced it will dissolve and be reconverted into carbonic acid (H2CO3) by carbonic anhydrase in the red blood cell . it will then ionize and be exported in the plasma via the HCO3 / Cl transporter
146
when the red blood cell reaches the lungs HCO3 is transported back into the red blood cell , then is converted into .. and .. by ........ and the ...... is released in the lungs
H2O and CO2
CO2
147
why is carbonic andrahase so important?
because we could not get rid of CO2 without it
148
what are the four major tissue types
nervous tissue, epithelial tissue , muscle tissue and connective tissue
149
what is the matrix made out of in connective tissue
fibers (collagen, elastic fiber and reticular fibers) and ground substance (polysaccharide and protien complexes for most connective tissue
150
what is responsible for the structural characteristics of connective tissue
fibers
- collagen
- elastic fibres (elasticity)
151
what is ground substance in connective tissue
can be simple globular protiens
can be aggregates of protiens and large polysaccaharides
both are surrounded by water
152
fibroblasts do what to the matrix
produce matrix
153
macrophages do what in the matrix
immune cell for repair and defence
154
adpocytes store
fat (triglycerides)
155
enteric ganglia help regulate what?
activity of the gut
156
microgalil (
clean up debris
157
schwann cells
insulation
158
astrocytes
support neurons
159
oligodendrocytes
insulate axons
160
metabolic organelle without a membrane
ribosome
161
structural organelle without membrane
microfilaments
intermediate filamaments
microtubules
centrosomes
162
rough ER is responsible for
protien synthesis , modification, trafficing
163
smooth ER is responsible for
lipid synthesis , general metabolic functions, calcium physiology
164
the golgi apparatus is
a site of protein modification and carb synthesis that works together with ER
protiens - formed by attaching carb to protein that have been transported from rER
165
mitochondria is responsible for
redox reactions that drive the phosphorlization of ADP and ATP
- heme production
- urea cycle
- calcium homeostasis
166
vesicles have ..... functions and vacuoles have ..... functions
transport, storage
167
ribosome is an organelle ......... that uses mRNA to accomplish
without membrane , protien translation
168
whats the difference of free ribosomes verus ribosomes attached to rER
free - translation of cytosolic proteins
rER - translation of protiens that will be modified and transported in ER
169
actin filaments are responsible for ....
shape of the microvilli
170
desmin is organised to
provide strength across the cell
171
a very large number of tiny vessels
capillaries
172
large capacity vessles
venules and veins
173
stroke volume x heart rate = ?
flow (cardiac output)
174
what are the major baroreceptors
carotoid arteries
arch of the aorta
175
gas and pH sensors are found in ...
the same location as baroreceptors
carotoid arteries
arch of the aorta
176
cerebral cortex respiratory role
voluntary control
177
hypothalamus respiratory role
regulates breathing on emotional states, pain, body temp
178
proprioceptors respiratory role
muscles and joints move, sends signals to brain stem - ventillation changes in inticipation of increased MSK o2 or co2 needs
179
chemoreceptors respiratory role
increase ventilation when arterial oxygen drops amd carbon dioxide increases
180
medulla and pons respiratory role
regulate activity of major muscles for ventillation
